MAGENTA Non-Hispanic White Blood Gene Expression QTL #

Multi-Ancestry Genomics, Epigenomics, and Transcriptomics of Alzheimer’s (MAGENTA) Project: Participants include 465 individuals (AA – 113 with AD, 118 cognitively intact controls; NHW – 116 with AD, 118 controls) ascertained by the John P. Hussman Institute for Human Genomics (HIHG) at the University of Miami Miller School of Medicine (Miami, FL), North Carolina A&T State University (Greensboro, NC), and Case Western Reserve University (Cleveland, OH). Participants were ascertained as part of the ADSP Follow-up Study and included both cases (>65 years of age of onset) and controls (>65 years of age at age of exam). All participants were adjudicated by a clinical panel with expertise in AD related disorders and classified as AD according to standard criteria developed by the National Institute of Aging and the Alzheimer’s Association.

Contact #

Makaela Mews (analyst; mxm1368@case.edu); Dr. William S. Bush ( wsb36@case.edu); Dr. Anthony J. Griswold (Griswold, Anthony J agriswold@miami.edu)

Study Overview #

Sample information: MAGENTA/MAGENTA_NHW_eqtl_sample_attributes.csv.
Lab protocol: MAGENTA/MAGENTA_NHW_eqtl_lab_protocol.csv.
Computational protocol: MAGENTA/MAGENTA_NHW_eqtl_computational_protocol.csv.
QTL summary statistics output: MAGENTA/MAGENTA_NHW_expression.qtl_results.csv.
Fine-mapping results individual level data model: ####/####.susie.csv.
Fine-mapping results summary statistics model: ####/####.susie_rss.csv.
Colocalization with AD GWAS: ####/####.susie_coloc.csv. where “Sample information” is a CSV file containing sample attributes / complete set of covariates for the exact samples used in the QTL study; “Lab protocol” is a CSV file containing the experimental protocol information to process the samples; “Computational protocol” is a CSV file containing the computational protocol information to process the samples; “QTL summary statistics output” is the list of QTL summary statistics results; “Fine-mapping results individual level data model” is the list of fine-mapped QTL using individual level phenotype and genotype data input for SuSiE model. “Fine-mapping results summary statistics model” uses QTL summary statistics for SuSiE RSS model. “Colocalization with AD GWAS” is the list of colocalization analysis with different AD GWAS publications and data-sets using coloc model on SuSiE results.

Analysis Status #

TransQTL association: Need to be updated with new covariate files.

Dataset Details #

Path(s) to genotype matrix #

Here please document the exact genotype matrix used for QTL calling.

Path(s) to the data on your local cluster where you analyzed the data.
TensorQTL - cis: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/nhw_239/geno/by_chr/nhw_chr_1_22.no_rel.filtered.plink_files_list.txt
TensorQTL - trans: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/nhw_239/geno/geno_final/rerun/nhw_chr_1_22.no_rel.filtered.bed
NIAGADS FTP, /ftp_fgc_xqtl/projects/... A summary of the genotype data including size used for TensorQTL - cis:

$ ls -lh *{bed,bim,fam,txt}
-rw-r--r-- 1 mxm1368 wsb36  29M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.10.bed
-rw-r--r-- 1 mxm1368 wsb36  19M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.10.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.10.fam
-rw-r--r-- 1 mxm1368 wsb36  28M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.11.bed
-rw-r--r-- 1 mxm1368 wsb36  18M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.11.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.11.fam
-rw-r--r-- 1 mxm1368 wsb36  28M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.12.bed
-rw-r--r-- 1 mxm1368 wsb36  18M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.12.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.12.fam
-rw-r--r-- 1 mxm1368 wsb36  21M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.13.bed
-rw-r--r-- 1 mxm1368 wsb36  13M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.13.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.13.fam
-rw-r--r-- 1 mxm1368 wsb36  19M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.14.bed
-rw-r--r-- 1 mxm1368 wsb36  12M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.14.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.14.fam
-rw-r--r-- 1 mxm1368 wsb36  16M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.15.bed
-rw-r--r-- 1 mxm1368 wsb36  10M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.15.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.15.fam
-rw-r--r-- 1 mxm1368 wsb36  18M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.16.bed
-rw-r--r-- 1 mxm1368 wsb36  11M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.16.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.16.fam
-rw-r--r-- 1 mxm1368 wsb36  16M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.17.bed
-rw-r--r-- 1 mxm1368 wsb36 9.3M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.17.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.17.fam
-rw-r--r-- 1 mxm1368 wsb36  17M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.18.bed
-rw-r--r-- 1 mxm1368 wsb36  11M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.18.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.18.fam
-rw-r--r-- 1 mxm1368 wsb36  13M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.19.bed
-rw-r--r-- 1 mxm1368 wsb36 7.9M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.19.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.19.fam
-rw-r--r-- 1 mxm1368 wsb36  44M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.1.bed
-rw-r--r-- 1 mxm1368 wsb36  27M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.1.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.1.fam
-rw-r--r-- 1 mxm1368 wsb36  13M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.20.bed
-rw-r--r-- 1 mxm1368 wsb36 7.8M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.20.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.20.fam
-rw-r--r-- 1 mxm1368 wsb36 7.8M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.21.bed
-rw-r--r-- 1 mxm1368 wsb36 4.9M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.21.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.21.fam
-rw-r--r-- 1 mxm1368 wsb36 7.9M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.22.bed
-rw-r--r-- 1 mxm1368 wsb36 4.9M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.22.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.22.fam
-rw-r--r-- 1 mxm1368 wsb36  47M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.2.bed
-rw-r--r-- 1 mxm1368 wsb36  29M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.2.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.2.fam
-rw-r--r-- 1 mxm1368 wsb36  41M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.3.bed
-rw-r--r-- 1 mxm1368 wsb36  25M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.3.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.3.fam
-rw-r--r-- 1 mxm1368 wsb36  41M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.4.bed
-rw-r--r-- 1 mxm1368 wsb36  25M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.4.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.4.fam
-rw-r--r-- 1 mxm1368 wsb36  37M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.5.bed
-rw-r--r-- 1 mxm1368 wsb36  22M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.5.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.5.fam
-rw-r--r-- 1 mxm1368 wsb36  38M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.6.bed
-rw-r--r-- 1 mxm1368 wsb36  23M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.6.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.6.fam
-rw-r--r-- 1 mxm1368 wsb36  34M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.7.bed
-rw-r--r-- 1 mxm1368 wsb36  20M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.7.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.7.fam
-rw-r--r-- 1 mxm1368 wsb36  32M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.8.bed
-rw-r--r-- 1 mxm1368 wsb36  19M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.8.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.8.fam
-rw-r--r-- 1 mxm1368 wsb36  25M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.9.bed
-rw-r--r-- 1 mxm1368 wsb36  15M Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.9.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 23 14:26 nhw_chr_1_22.no_rel.filtered.9.fam
-rw-r--r-- 1 mxm1368 wsb36 2.3K Mar 23 14:27 nhw_chr_1_22.no_rel.filtered.plink_files_list.txt

A summary of the genotype data including size used for TensorQTL - trans:

$ ls -lh *.no_rel.filtered.{bim,bed,fam}
-rw-r--r-- 1 mxm1368 wsb36 563M Mar 22 13:30 nhw_chr_1_22.no_rel.filtered.bed
-rw-r--r-- 1 mxm1368 wsb36 344M Mar 22 13:30 nhw_chr_1_22.no_rel.filtered.bim
-rw-r--r-- 1 mxm1368 wsb36 5.9K Mar 22 13:30 nhw_chr_1_22.no_rel.filtered.fam

Path(s) to omics-data matrix #

Here please document the exact omics-data matrix used for QTL calling.

Path(s) to the data on your local cluster where you analyzed the data.
TensorQTL - cis: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/nhw_239/mol_phe/tmm_per_chr
TensorQTL - trans: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/nhw_239/mol_phe
NIAGADS FTP, /ftp_fgc_xqtl/projects/... A summary of the phenotype data including size used for TensorQTL - cis:

$ pwd
/mnt/pan/Data14/metabrain_lasso/rna_seq_norm/nhw_239/mol_phe/tmm_per_chr
$ ls -lh *.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  489K Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr10.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  718K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr11.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  722K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr12.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  224K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr13.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  508K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr14.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  436K Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr15.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  692K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr16.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  870K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr17.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  196K Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr18.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 1003K Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr19.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  1.4M Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr1.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  347K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr20.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  143K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr21.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  388K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr22.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  873K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr2.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  700K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr3.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  442K Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr4.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  576K Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr5.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  680K Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr6.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  688K Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr7.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  436K Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr8.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  506K Mar  2 19:06 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chr9.bed.gz
-rw-r--r-- 1 mxm1368 wsb36  417K Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chrX.bed.gz
-rw-r--r-- 1 mxm1368 wsb36   14K Mar  2 19:05 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.chrY.bed.gz

A summary of the phenotype data including size used for TensorQTL - trans:

$ pwd
/mnt/pan/Data14/metabrain_lasso/rna_seq_norm/nhw_239/mol_phe
$ ls -lh *tmm.expression.bed.gz
-rw-r--r-- 1 mxm1368 wsb36 14M Feb 27 18:02 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.bed.gz

Path(s) to covariate data matrix #

Here please document the exact covariate matrix used for QTL calling, including selected covariates from sample attribute file, genotype PC and phenotype hidden confounding factors computed in your previous analysis

Path(s) to the data on your local cluster where you analyzed the data.
Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/nhw_239/cov
NIAGADS FTP, /ftp_fgc_xqtl/projects/... A summary of the covariate data including size used for TensorQTL - cis & trans:

$ ls -lh *tmm.expression.cov_pca.resid.PEER.cov.gz
-rw-r--r-- 1 mxm1368 wsb36 91K Mar  2 19:01 nhw_no_rel.rnaseqc.low_expression_filtered.outlier_removed.tmm.expression.cov_pca.resid.PEER.cov.gz

Path(s) to QTL results #

TensorQTL - cis: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/nhw_239/tensorqtl/cis/plink_mac5
TensorQTL - trans: Bush Lab, server: rider.case.edu /mnt/pan/Data14/metabrain_lasso/rna_seq_norm/nhw_239/tensorqtl/trans/plink_mac5 A summary of the TensorQTL - cis data including size:

$ ls -lh
total 30G
-rw-r--r-- 1 mxm1368 wsb36 144M Mar 23 14:48 nhw_no_rel.10.cis_qtl_pairs.10.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 15:40 nhw_no_rel.10.cis_qtl_pairs.10.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  75K Mar 23 15:40 nhw_no_rel.10.cis_qtl_pairs.10.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 169K Mar 23 15:40 nhw_no_rel.10.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 801M Mar 23 14:51 nhw_no_rel.10.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 193M Mar 23 15:59 nhw_no_rel.11.cis_qtl_pairs.11.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 17:08 nhw_no_rel.11.cis_qtl_pairs.11.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36 113K Mar 23 17:08 nhw_no_rel.11.cis_qtl_pairs.11.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 246K Mar 23 17:08 nhw_no_rel.11.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.1G Mar 23 16:05 nhw_no_rel.11.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 201M Mar 23 16:58 nhw_no_rel.12.cis_qtl_pairs.12.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 17:25 nhw_no_rel.12.cis_qtl_pairs.12.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36 112K Mar 23 17:25 nhw_no_rel.12.cis_qtl_pairs.12.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 248K Mar 23 17:25 nhw_no_rel.12.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.2G Mar 23 17:02 nhw_no_rel.12.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36  69M Mar 23 16:01 nhw_no_rel.13.cis_qtl_pairs.13.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 16:24 nhw_no_rel.13.cis_qtl_pairs.13.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  38K Mar 23 16:24 nhw_no_rel.13.cis_qtl_pairs.13.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36  77K Mar 23 16:24 nhw_no_rel.13.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 378M Mar 23 16:02 nhw_no_rel.13.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 147M Mar 23 16:01 nhw_no_rel.14.cis_qtl_pairs.14.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 16:55 nhw_no_rel.14.cis_qtl_pairs.14.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  82K Mar 23 16:55 nhw_no_rel.14.cis_qtl_pairs.14.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 175K Mar 23 16:55 nhw_no_rel.14.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 845M Mar 23 16:05 nhw_no_rel.14.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 121M Mar 23 14:46 nhw_no_rel.15.cis_qtl_pairs.15.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 15:30 nhw_no_rel.15.cis_qtl_pairs.15.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  67K Mar 23 15:30 nhw_no_rel.15.cis_qtl_pairs.15.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 151K Mar 23 15:30 nhw_no_rel.15.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 654M Mar 23 14:49 nhw_no_rel.15.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 191M Mar 23 15:49 nhw_no_rel.16.cis_qtl_pairs.16.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 16:57 nhw_no_rel.16.cis_qtl_pairs.16.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36 100K Mar 23 16:57 nhw_no_rel.16.cis_qtl_pairs.16.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 238K Mar 23 16:57 nhw_no_rel.16.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.1G Mar 23 15:54 nhw_no_rel.16.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 232M Mar 23 16:12 nhw_no_rel.17.cis_qtl_pairs.17.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 17:20 nhw_no_rel.17.cis_qtl_pairs.17.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36 125K Mar 23 17:20 nhw_no_rel.17.cis_qtl_pairs.17.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 300K Mar 23 17:20 nhw_no_rel.17.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.3G Mar 23 16:19 nhw_no_rel.17.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36  63M Mar 23 14:41 nhw_no_rel.18.cis_qtl_pairs.18.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 14:59 nhw_no_rel.18.cis_qtl_pairs.18.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  31K Mar 23 14:59 nhw_no_rel.18.cis_qtl_pairs.18.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36  68K Mar 23 14:59 nhw_no_rel.18.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 339M Mar 23 14:42 nhw_no_rel.18.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 325M Mar 23 15:00 nhw_no_rel.19.cis_qtl_pairs.19.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 16:53 nhw_no_rel.19.cis_qtl_pairs.19.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36 144K Mar 23 16:53 nhw_no_rel.19.cis_qtl_pairs.19.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 344K Mar 23 16:53 nhw_no_rel.19.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.8G Mar 23 15:08 nhw_no_rel.19.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 345M Mar 23 15:07 nhw_no_rel.1.cis_qtl_pairs.1.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 17:12 nhw_no_rel.1.cis_qtl_pairs.1.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36 189K Mar 23 17:12 nhw_no_rel.1.cis_qtl_pairs.1.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 458K Mar 23 17:12 nhw_no_rel.1.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.9G Mar 23 15:17 nhw_no_rel.1.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 102M Mar 23 15:09 nhw_no_rel.20.cis_qtl_pairs.20.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 15:47 nhw_no_rel.20.cis_qtl_pairs.20.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  54K Mar 23 15:47 nhw_no_rel.20.cis_qtl_pairs.20.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 119K Mar 23 15:47 nhw_no_rel.20.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 555M Mar 23 15:11 nhw_no_rel.20.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36  48M Mar 23 15:40 nhw_no_rel.21.cis_qtl_pairs.21.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 15:54 nhw_no_rel.21.cis_qtl_pairs.21.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  25K Mar 23 15:54 nhw_no_rel.21.cis_qtl_pairs.21.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36  48K Mar 23 15:54 nhw_no_rel.21.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 241M Mar 23 15:41 nhw_no_rel.21.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 112M Mar 23 16:35 nhw_no_rel.22.cis_qtl_pairs.22.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 17:10 nhw_no_rel.22.cis_qtl_pairs.22.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  50K Mar 23 17:10 nhw_no_rel.22.cis_qtl_pairs.22.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 134K Mar 23 17:10 nhw_no_rel.22.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 647M Mar 23 16:38 nhw_no_rel.22.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 234M Mar 23 16:28 nhw_no_rel.2.cis_qtl_pairs.2.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 17:24 nhw_no_rel.2.cis_qtl_pairs.2.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36 124K Mar 23 17:24 nhw_no_rel.2.cis_qtl_pairs.2.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 300K Mar 23 17:24 nhw_no_rel.2.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.3G Mar 23 16:34 nhw_no_rel.2.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 188M Mar 23 16:40 nhw_no_rel.3.cis_qtl_pairs.3.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 17:23 nhw_no_rel.3.cis_qtl_pairs.3.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36 102K Mar 23 17:23 nhw_no_rel.3.cis_qtl_pairs.3.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 240K Mar 23 17:23 nhw_no_rel.3.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.1G Mar 23 16:45 nhw_no_rel.3.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 133M Mar 23 14:47 nhw_no_rel.4.cis_qtl_pairs.4.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 15:35 nhw_no_rel.4.cis_qtl_pairs.4.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  69K Mar 23 15:35 nhw_no_rel.4.cis_qtl_pairs.4.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 153K Mar 23 15:35 nhw_no_rel.4.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 752M Mar 23 14:49 nhw_no_rel.4.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 163M Mar 23 14:49 nhw_no_rel.5.cis_qtl_pairs.5.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 15:50 nhw_no_rel.5.cis_qtl_pairs.5.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  81K Mar 23 15:50 nhw_no_rel.5.cis_qtl_pairs.5.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 198K Mar 23 15:50 nhw_no_rel.5.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 886M Mar 23 14:53 nhw_no_rel.5.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 248M Mar 23 14:53 nhw_no_rel.6.cis_qtl_pairs.6.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 16:21 nhw_no_rel.6.cis_qtl_pairs.6.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  85K Mar 23 16:21 nhw_no_rel.6.cis_qtl_pairs.6.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 235K Mar 23 16:21 nhw_no_rel.6.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.5G Mar 23 15:00 nhw_no_rel.6.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 196M Mar 23 14:52 nhw_no_rel.7.cis_qtl_pairs.7.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 16:04 nhw_no_rel.7.cis_qtl_pairs.7.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  98K Mar 23 16:04 nhw_no_rel.7.cis_qtl_pairs.7.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 237K Mar 23 16:04 nhw_no_rel.7.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 1.1G Mar 23 14:57 nhw_no_rel.7.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 132M Mar 23 14:47 nhw_no_rel.8.cis_qtl_pairs.8.parquet
-rw-r--r-- 1 mxm1368 wsb36  285 Mar 23 15:33 nhw_no_rel.8.cis_qtl_pairs.8.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  66K Mar 23 15:33 nhw_no_rel.8.cis_qtl_pairs.8.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 150K Mar 23 15:33 nhw_no_rel.8.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 712M Mar 23 14:49 nhw_no_rel.8.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36 150M Mar 23 15:47 nhw_no_rel.9.cis_qtl_pairs.9.parquet
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 23 16:39 nhw_no_rel.9.cis_qtl_pairs.9.parquet.stderr
-rw-r--r-- 1 mxm1368 wsb36  73K Mar 23 16:39 nhw_no_rel.9.cis_qtl_pairs.9.parquet.stdout
-rw-r--r-- 1 mxm1368 wsb36 174K Mar 23 16:39 nhw_no_rel.9.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36 793M Mar 23 15:51 nhw_no_rel.9.norminal.cis_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36  106 Mar 23 17:26 nhw_no_rel.emprical.cis_sumstats.summary
-rw-r--r-- 1 mxm1368 wsb36 5.9M Mar 23 17:26 nhw_no_rel.emprical.cis_sumstats.txt
-rw-r--r-- 1 mxm1368 wsb36  311 Mar 23 17:25 TensorQTL.cis._column_info.txt
-rw-r--r-- 1 mxm1368 wsb36 5.0K Mar 23 17:25 TensorQTL.cis._recipe.tsv
-rw-r--r-- 1 mxm1368 wsb36  18K Mar 23 17:26 TensorQTL.cis._recipe.tsv.stderr
-rw-r--r-- 1 mxm1368 wsb36   46 Mar 23 17:25 TensorQTL.cis._recipe.tsv.stdout

A summary of the TensorQTL - trans data including size:

$ ls -lh
total 6.5M
-rw-r--r-- 1 mxm1368 wsb36 4.9M Mar 24 09:42 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.norminal.trans_long_table.txt
-rw-r--r-- 1 mxm1368 wsb36  360 Mar 24 09:42 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.norminal.trans_long_table.txt.stderr
-rw-r--r-- 1 mxm1368 wsb36  56K Mar 24 09:42 nhw_gene_tpm_prep_v2.low_expression_filtered.outlier_removed.tmm.expression.norminal.trans_long_table.txt.stdout
-rw-r--r-- 1 mxm1368 wsb36  189 Mar 24 09:42 TensorQTL.trans._column_info.txt
-rw-r--r-- 1 mxm1368 wsb36  323 Mar 24 09:42 TensorQTL.trans._recipe.tsv

Path(s) to fine-mapping with SuSiE model #

Path(s) to fine-mapping with SuSiE RSS model #

Path(s) to colocalization with SuSiE-coloc #

Links to QTL analysis notebooks #

Please list the links to analysis notebooks in the order you executed our pipeline:

Genotype processing: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Bush_CWRU/magenta_nhw_eqtl_genotype_processing.ipynb
Phenotype processing: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Bush_CWRU/magenta_nhw_eqtl_phenotype_processing.ipynb
Covariate processing: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Bush_CWRU/magenta_nhw_eqtl_covariate_processing.ipynb
TensorQTL analysis: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Bush_CWRU/magenta_nhw_eqtl_tensorqtl.ipynb
Complete analysis pipeline: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Bush_CWRU/magenta_nhw_eqtl_complete_analysis.ipynb